Small-angle X-ray scattering studies of the oligomeric state and quaternary structure of the trifunctional proline utilization A (PutA) flavoprotein from Escherichia coli

Journal of Biological Chemistry

Volumn 286, Issue 50, 2011, Pages 43144-43153

  Singh, Ranjan K ^a   Larson, John D ^a   Zhu, Weidong ^c   Rambo, Robert P ^d   Hura, Greg L ^d   Becker, Donald F ^c   Tanner, John J ^a,b  

^a UNIVERSITY OF MISSOURI   (United States)

^b University of Missouri   (United States)

^c UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE DEHYDROGENASE; AMINO ACID SEQUENCE; C-TERMINAL DOMAINS; CATALYTIC ACTIVE SITES; CATALYTIC INTERMEDIATES; DELETION ANALYSIS; DNA-BINDING; DNA-BINDING DOMAIN; GRAM-NEGATIVE BACTERIA; INTERNAL SUBSTRATE; N-TERMINALS; OLIGOMERIC STATE; PROLINE UTILIZATION; QUATERNARY STRUCTURE; RIGID-BODY MODELING; SHAPE RECONSTRUCTION; SMALL ANGLE X-RAY SCATTERING; STRUCTURAL INFORMATION;

ALDEHYDES; AMINO ACIDS; BACTERIA; BINDING SITES; CARBOXYLATION; CYLINDERS (SHAPES); DNA; ESCHERICHIA COLI; GENES; OLIGOMERIZATION; OLIGOMERS; SCATTERING; TRANSCRIPTION; X RAY SCATTERING; X RAYS;

CRYSTAL STRUCTURE;

ALDEHYDE DEHYDROGENASE; DIMER; ESCHERICHIA COLI PROTEIN; FLAVOPROTEIN; OLIGOMER; PYRROLINE 5 CARBOXYLATE DEHYDROGENASE; TRIFUNCTIONAL PROLINE UTILIZATION A PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; ESCHERICHIA COLI; GENE CONTROL; GENETIC TRANSCRIPTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN QUATERNARY STRUCTURE; RADIATION SCATTERING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; ESCHERICHIA COLI; MEMBRANE PROTEINS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; SCATTERING, SMALL ANGLE; X-RAYS;

EID: 83355169696     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.292474     Document Type: Article

References (51)

1. Tanner, J. J. (2008) Amino Acids 35, 719-730
2. Zhou, Y., Zhu, W., Bellur, P. S., Rewinkel, D., and Becker, D. F. (2008) Amino Acids 35, 711-718
3. Menzel, R., and Roth, J. (1981) J. Mol. Biol. 148, 21-44
4. Maloy, S. R., and Roth, J. R. (1983) J. Bacteriol. 154, 561-568
5. Wood, J. M. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 373-377
6. Ostrovsky de Spicer, P., and Maloy, S. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 4295-4298
7. Muro-Pastor, A. M., and Maloy, S. (1995) J. Biol. Chem. 270, 9819-9827
8. Vílchez, S., Manzanera, M., and Ramos, J. L. (2000) Appl. Environ. Microbiol. 66, 5221-5225
9. Zhou, Y., Larson, J. D., Bottoms, C. A., Arturo, E. C., Henzl, M. T., Jenkins, J. L., Nix, J. C., Becker, D. F., and Tanner, J. J. (2008) J. Mol. Biol. 381, 174-188
10. Brown, E. D., and Wood, J. M. (1993) J. Biol. Chem. 268, 8972-8979
11. Becker, D. F., and Thomas, E. A. (2001) Biochemistry 40, 4714-4721
12. Vinod, M. P., Bellur, P., and Becker, D. F. (2002) Biochemistry 41, 6525-6532
13. Zhu, W., and Becker, D. F. (2003) Biochemistry 42, 5469-5477
14. Lee, Y. H., Nadaraia, S., Gu, D., Becker, D. F., and Tanner, J. J. (2003) Nat. Struct. Biol. 10, 109-114
15. Zhang, W., Zhou, Y., and Becker, D. F. (2004) Biochemistry 43, 13165-13174
16. Zhang, M., White, T. A., Schuermann, J. P., Baban, B. A., Becker, D. F., and Tanner, J. J. (2004) Biochemistry 43, 12539-12548
17. Zhu, W., and Becker, D. F. (2005) Biochemistry 44, 12297-12306
18. Srivastava, D., Schuermann, J. P., White, T. A., Krishnan, N., Sanyal, N., Hura, G. L., Tan, A., Henzl, M. T., Becker, D. F., and Tanner, J. J. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 2878-2883
19. Larson, J. D., Jenkins, J. L., Schuermann, J. P., Zhou, Y., Becker, D. F., and Tanner, J. J. (2006) Protein Sci. 15, 2630-2641
20. Zhang, W., Zhang, M., Zhu, W., Zhou, Y., Wanduragala, S., Rewinkel, D., Tanner, J. J., and Becker, D. F. (2007) Biochemistry 46, 483-491
21. Ostrander, E. L., Larson, J. D., Schuermann, J. P., and Tanner, J. J. (2009) Biochemistry 48, 951-959
22. Srivastava, D., Zhu, W., Johnson, W. H., Jr., Whitman, C. P., Becker, D. F., and Tanner, J. J. (2010) Biochemistry 49, 560-569
23. Ratzkin, B., and Roth, J. (1978) J. Bacteriol. 133, 744-754
24. Brown, E. D., and Wood, J. M. (1992) J. Biol. Chem. 267, 13086-13092
25. Zhu, W., Gincherman, Y., Docherty, P., Spilling, C. D., and Becker, D. F. (2002) Arch. Biochem. Biophys. 408, 131-136
26. Hura, G. L., Menon, A. L., Hammel, M., Rambo, R. P., Poole, F. L., 2nd, Tsutakawa, S. E., Jenney, F. E., Jr., Classen, S., Frankel, K. A., Hopkins, R. C., Yang, S. J., Scott, J. W., Dillard, B. D., Adams, M. W., and Tainer, J. A. (2009) Nat. Methods 6, 606-612
27. Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H., and Svergun, D. I. (2003) J. Appl. Crystallogr. 36, 1277-1282
28. Svergun, D. I. (1992) J. Appl. Crystallogr. 25, 495-503
29. Mylonas, E., and Svergun, D. I. (2007) J. Appl. Crystallogr. 40, s245-s249
30. Svergun, D. I., Petoukhov, M. V., and Koch, M. H. (2001) Biophys. J. 80, 2946-2953
31. Volkov, V. V., and Svergun, D. I. (2003) J. Appl. Crystallogr. 36, 860-864
32. Wriggers, W. (2010) Biophys. Rev. 2, 21-27
33. Kozin, M. B., and Svergun, D. I. (2001) J. Appl. Crystallogr. 34, 33-41
34. Zhang, Y. (2008) BMC Bioinformatics 9, 40
35. Arnold, K., Bordoli, L., Kopp, J., and Schwede, T. (2006) Bioinformatics 22, 195-201
36. Chacón, P., and Wriggers, W. (2002) J. Mol. Biol. 317, 375-384
37. Schneidman-Duhovny, D., Hammel, M., and Sali, A. (2010) Nucleic Acids Res. 38, W540-544
38. de Bakker, P. I., DePristo, M. A., Burke, D. F., and Blundell, T. L. (2003) Proteins 51, 21-40
39. Potterton, E., Briggs, P., Turkenburg, M., and Dodson, E. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1131-1137
40. Williams, I., and Frank, L. (1975) Anal. Biochem. 64, 85-97
41. Easley, K. E., Sommer, B. J., Boanca, G., Barycki, J. J., and Simpson, M. A. (2007) Biochemistry 46, 369-378
42. Rambo, R. P., and Tainer, J. A. (2011) Biopolymers 95, 559-571
43. Schreiter, E. R., and Drennan, C. L. (2007) Nat. Rev. Microbiol. 5, 710-720
44. Muro-Pastor, A. M., Ostrovsky, P., and Maloy, S. (1997) J. Bacteriol. 179, 2788-2791
45. Sophos, N. A., and Vasiliou, V. (2003) Chem. Biol. Interact. 143-144, 5-22
46. Yoshida, A., Rzhetsky, A., Hsu, L. C., and Chang, C. (1998) Eur. J. Biochem. 251, 549-557
47. Liu, Z. J., Sun, Y. J., Rose, J., Chung, Y. J., Hsiao, C. D., Chang, W. R., Kuo, I., Perozich, J., Lindahl, R., Hempel, J., and Wang, B. C. (1997) Nat. Struct. Biol. 4, 317-326
48. Moore, S. A., Baker, H. M., Blythe, T. J., Kitson, K. E., Kitson, T. M., and Baker, E. N. (1998) Structure 6, 1541-1551
49. Steinmetz, C. G., Xie, P., Weiner, H., and Hurley, T. D. (1997) Structure 5, 701-711
50. Inagaki, E., Ohshima, N., Takahashi, H., Kuroishi, C., Yokoyama, S., and Tahirov, T. H. (2006) J. Mol. Biol. 362, 490-501
51. Surber, M. W., and Maloy, S. (1998) Arch. Biochem. Biophys. 354, 281-287